If you see this message after the page is completely loaded, then JavaScript is not supported or disabled in your browser. Please consider enabling JavaScript for this site.

MK13_HUMAN_1_352

Mitogen-activated protein kinase 13 [Protein kinase superfamily. CMGC Ser/Thr protein kinase family. MAP kinase subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (MK13_HUMAN):D: Protein kinase (36, 39, 52, 54, 68, 72, 75, 76, 79, 84, 85, 107:110, 146, 148, 166:171)36, 39, 52, 54, 68, 72, 75, 76, 79, 84, 85, 107:110, 146, 148, 166:171

Full PDB list

3coi, 4eyj, 4eym, 4myg, 4yno, 5ekn, 5eko (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
V
3
9
A
5
2
K
5
4
R
6
8
E
7
2
L
7
5
L
7
6
M
7
9
V
8
4
I
8
5
M
1
0
7
P
1
0
8
F
1
0
9
M
1
1
0
V
1
4
6
H
1
4
8
I
1
6
6
L
1
6
7
D
1
6
8
F
1
6
9
G
1
7
0
L
1
7
1
[1]4eym.a 0rx28 . . . . . . . . . . . . . . . . . . . . . .
[1]4yno.a none . . . . . . . . . . . . . . . . . . . . . .
[1]5eko.a n1728 . . . . . . . . . . . . . . . . . . . . . .
[2]4eyj.a n6127 . . . . . . . . . . . . . . . . . . . . . .
[2]5ekn.a n5827 . . . . . . . . . . . . . . . . . . . . - -

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Site contact map

[download in TSV format]
   
PDB.ch
A1
Y
3
6
V
3
9
A
5
2
K
5
4
R
6
8
E
7
2
L
7
5
L
7
6
M
7
9
V
8
4
I
8
5
M
1
0
7
P
1
0
8
F
1
0
9
M
1
1
0
V
1
4
6
H
1
4
8
I
1
6
6
L
1
6
7
D
1
6
8
F
1
6
9
G
1
7
0
L
1
7
1
[1]4eym.a . . . . . . . . . . . . . . . . . . . . * . .
[1]4yno.a . . . . * . . . . . . . . . . . . . . . * . *
[1]5eko.a . . . . . . . . . . . . . . . . . . . . * . .
[2]4eyj.a . . . . * . . . . . . . . . . . . . . . . . .
[2]5ekn.a . . . . . . . . . . . . . . . . . . . . . - -

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X X X X X  clash
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Pocket-ligand steric compatibility

Ligands (x) vs pockets (y) colored by number of steric clashes

zoom: [−] [+]; [view as image]; [download as text]

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
4eym.a:0rx
4yno.a is apo
5eko.a:n17
4eyj.a:n61
5ekn.a:n58
[1] 4eym.a
0
- 0 4.9 5.0
[1] 4yno.a 3.9
-
3.6 5.6 5.7
[1] 5eko.a 0.1 -
0
5.3 4.8
[2] 4eyj.a 0.8 - 1.1
0
0.1
[2] 5ekn.a 0.1 - 0.1 0
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
4eym.a
4yno.a
5eko.a
4eyj.a
5ekn.a
[1] 4eym.a
0
.17 .02 .25 .20
[1] 4yno.a .17
0
.18 .32 .36
[1] 5eko.a .02 .18
0
.27 .22
[2] 4eyj.a .25 .32 .27
0
.04
[2] 5ekn.a .20 .36 .22 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.3 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
4eym.a
4yno.a
5eko.a
4eyj.a
5ekn.a
[1] 4eym.a
0
0.6 0.4 2.8 1.7
[1] 4yno.a 0.6
0
0.5 3.0 1.8
[1] 5eko.a 0.4 0.5
0
3.1 1.8
[2] 4eyj.a 2.8 3.0 3.1
0
0.6
[2] 5ekn.a 1.7 1.8 1.8 0.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
4eym.a
4yno.a
5eko.a
4eyj.a
5ekn.a
[1] 4eym.a
0
1.3 0.6 3.2 2.5
[1] 4yno.a 1.3
0
1.1 3.3 2.7
[1] 5eko.a 0.6 1.1
0
3.3 2.5
[2] 4eyj.a 3.2 3.3 3.3
0
0.9
[2] 5ekn.a 2.5 2.7 2.5 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

loading...